> Can you provide a usage scenario for including history_id in the tool
A simple example is the creation of a full history based log file.
My more detailed need is to parallel an existing analysis pipeline in
galaxy, using the same underlying code. Reusing the same code from within
galaxy has the great advantage of ensuring exactly the same process is run,
allowing the "official" analysis to be repeated by outsiders. This
pipeline works on a number of inputs (paired end reads, multiple
replicates, etc.) and goes through a number of intervening steps where
massive temporary files may be reused in several steps, then ultimately
deleted after obtaining final results. The existing pipeline, outside of
galaxy, creates these shared files in a temporary directory, exclusive to
the "experiment" being run. In Galaxy however, ensuring that an
"experiment" named by one user will not collide with one named by another
user, accidentally overwriting existing files becomes a great deal easier
if the temporary experiment directories have history_id based names. Since
the histories could be shared among multiple users, the user_id will not be
effective. Within a single history, steps can be rerun, new inputs can be
introduced and overwriting temporary files is entirely appropriate. But
collisions between 2 separate histories would not be desirable at all.
On Mon, Sep 23, 2013 at 7:31 PM, Jeremy Goecks <jeremy.goe...@emory.edu>wrote:
> At line ~694:
> incoming['__user_name__'] = user_name
> + if job.history and job.history.id:
> + incoming['__history_id__'] = job.history.id
> + else:
> + incoming['__history_id__'] = 'unknown'
> I have tested this change and it appears to give me exactly what I want.
> My question: does this change appear correct
> Yes, the change is correct.
> and can it be incorporated into the main galaxy code-base?
> Can you provide a usage scenario for including history_id in the tool dict?
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